Propose 36 literature-backed ENVIRONMENT + METABOLISM traits

data/traits/environment/arsenic_tolerant.yaml

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+identifier: traitmech:000017
+label: arsenic tolerant
+definition: A metalloid tolerance in which an organism grows in the presence of
+  elevated arsenic (arsenite/arsenate) concentrations, typically via the ars operon,
+  whose ArsB pump extrudes arsenite from the cytoplasm.
+definition_source: DOI:10.3389/fmicb.2018.02473
+trait_category: ENVIRONMENT
+term_kind: CLASS
+mapping_status: PROPOSED
+parent_traits:
+- traitmech:000012
+synonyms:
+- synonym_text: arsenic resistant
+  synonym_type: RELATED_SYNONYM
+  source: DOI:10.3389/fmicb.2018.02473
+evidence:
+- reference: DOI:10.3389/fmicb.2018.02473
+  snippet: ArsB is an integral membrane protein able to extrude arsenite from the
+    cell cytoplasm, thus diminishing arsenite accumulation
+  notes: Review supports the ars operon as a near-ubiquitous arsenic-resistance
+    determinant, "more common than genes for tryptophan biosynthesis".
+- reference: DOI:10.3389/fmicb.2020.00047
+  snippet: C. metallidurans BS1 conferred resistance to Zn2+ displaying a MIC of 20
+    mM, Cd2+ (2.5 mM), Co2+ (20mM), Ni2+ (8 mM), As3+ (3.5 mM), Cu2+ (5 mM), Au3+ (1
+    uM) and Pb2+ (1.7 mM)
+  notes: 'Organism example: Cupriavidus metallidurans BS1 tolerates arsenite (As3+)
+    to a MIC of 3.5 mM.'
+curation_history:
+- timestamp: '2026-05-28T00:00:00Z'
+  curator: claude
+  action: PROPOSED_FROM_RESEARCH
+  changes: Proposed candidate ENVIRONMENT trait (arsenic/metalloid tolerance) from
+    literature research; sub-variant of metal tolerant.
+  llm_assisted: true

data/traits/environment/cadmium_tolerant.yaml

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+identifier: traitmech:000013
+label: cadmium tolerant
+definition: A metal tolerance in which an organism grows in the presence of elevated
+  cadmium (Cd2+) concentrations, typically via cation-efflux resistance systems such
+  as the czc determinant.
+definition_source: PMID:12829273
+trait_category: ENVIRONMENT
+term_kind: CLASS
+mapping_status: PROPOSED
+parent_traits:
+- traitmech:000012
+evidence:
+- reference: DOI:10.1111/j.1365-2958.2009.06792.x
+  snippet: CzcP exports transition metals Zn(2+), Cd(2+) and Co(2+)
+  notes: The cobalt-zinc-cadmium (czc) efflux system of Cupriavidus metallidurans
+    confers cadmium resistance.
+- reference: DOI:10.3389/fmicb.2020.00047
+  snippet: C. metallidurans BS1 conferred resistance to Zn2+ displaying a MIC of 20
+    mM, Cd2+ (2.5 mM), Co2+ (20mM), Ni2+ (8 mM), As3+ (3.5 mM), Cu2+ (5 mM), Au3+ (1
+    uM) and Pb2+ (1.7 mM)
+  notes: 'Organism example: Cupriavidus metallidurans BS1 tolerates cadmium to a MIC
+    of 2.5 mM.'
+curation_history:
+- timestamp: '2026-05-28T00:00:00Z'
+  curator: claude
+  action: PROPOSED_FROM_RESEARCH
+  changes: Proposed candidate ENVIRONMENT trait (cadmium tolerance) from literature
+    research; metal-specific sub-variant of metal tolerant.
+  llm_assisted: true

data/traits/environment/cobalt_tolerant.yaml

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+identifier: traitmech:000015
+label: cobalt tolerant
+definition: A metal tolerance in which an organism grows in the presence of elevated
+  cobalt (Co2+) concentrations, typically via cation-efflux resistance systems such
+  as the czc and cnr determinants.
+definition_source: PMID:12829273
+trait_category: ENVIRONMENT
+term_kind: CLASS
+mapping_status: PROPOSED
+parent_traits:
+- traitmech:000012
+evidence:
+- reference: DOI:10.1111/j.1365-2958.2009.06792.x
+  snippet: CzcP exports transition metals Zn(2+), Cd(2+) and Co(2+)
+  notes: The cobalt-zinc-cadmium (czc) efflux system of Cupriavidus metallidurans
+    confers cobalt resistance.
+- reference: DOI:10.3389/fmicb.2020.00047
+  snippet: C. metallidurans BS1 conferred resistance to Zn2+ displaying a MIC of 20
+    mM, Cd2+ (2.5 mM), Co2+ (20mM), Ni2+ (8 mM), As3+ (3.5 mM), Cu2+ (5 mM), Au3+ (1
+    uM) and Pb2+ (1.7 mM)
+  notes: 'Organism example: Cupriavidus metallidurans BS1 tolerates cobalt to a MIC
+    of 20 mM.'
+curation_history:
+- timestamp: '2026-05-28T00:00:00Z'
+  curator: claude
+  action: PROPOSED_FROM_RESEARCH
+  changes: Proposed candidate ENVIRONMENT trait (cobalt tolerance) from literature
+    research; metal-specific sub-variant of metal tolerant.
+  llm_assisted: true

data/traits/environment/copper_tolerant.yaml

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+identifier: traitmech:000018
+label: copper tolerant
+definition: A metal tolerance in which an organism grows in the presence of elevated
+  copper (Cu2+/Cu+) concentrations, typically via the cue, cus, pco, and cop systems
+  and ATPase-driven cytoplasmic copper efflux.
+definition_source: DOI:10.1007/s10565-013-9262-1
+trait_category: ENVIRONMENT
+term_kind: CLASS
+mapping_status: PROPOSED
+parent_traits:
+- traitmech:000012
+synonyms:
+- synonym_text: copper resistant
+  synonym_type: RELATED_SYNONYM
+  source: DOI:10.1007/s10565-013-9262-1
+evidence:
+- reference: DOI:10.1007/s10565-013-9262-1
+  snippet: ATPase-driven copper efflux seems to be the main mechanism responsible
+    for cytoplasmic copper detoxification in until now studied bacteria
+  notes: Review supports active efflux via the cue, cus, pco, and cop systems as the
+    basis of bacterial copper tolerance.
+- reference: DOI:10.3389/fmicb.2020.00047
+  snippet: C. metallidurans BS1 conferred resistance to Zn2+ displaying a MIC of 20
+    mM, Cd2+ (2.5 mM), Co2+ (20mM), Ni2+ (8 mM), As3+ (3.5 mM), Cu2+ (5 mM), Au3+ (1
+    uM) and Pb2+ (1.7 mM)
+  notes: 'Organism example: Cupriavidus metallidurans BS1 tolerates copper (Cu2+) to
+    a MIC of 5 mM.'
+curation_history:
+- timestamp: '2026-05-28T00:00:00Z'
+  curator: claude
+  action: PROPOSED_FROM_RESEARCH
+  changes: Proposed candidate ENVIRONMENT trait (copper tolerance) from literature
+    research; metal-specific sub-variant of metal tolerant.
+  llm_assisted: true

data/traits/environment/desiccation_tolerant.yaml

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+identifier: traitmech:000010
+label: desiccation tolerant
+definition: An environmental tolerance in which an organism survives extreme water
+  loss and resumes growth after rehydration (anhydrobiosis), protecting cellular
+  macromolecules during drying.
+definition_source: DOI:10.3390/microorganisms10020432
+trait_category: ENVIRONMENT
+term_kind: CLASS
+mapping_status: PROPOSED
+parent_traits:
+- METPO:1000059
+synonyms:
+- synonym_text: anhydrobiotic
+  synonym_type: RELATED_SYNONYM
+  source: DOI:10.3390/microorganisms10020432
+evidence:
+- reference: DOI:10.3390/microorganisms10020432
+  snippet: Anhydrobiosis (gr. life without water) is predominantly described as the
+    ability of some organisms to lose all or almost all water and enter a state of
+    suspension where the metabolism comes to a reversible standstill
+  notes: Bacterial anhydrobiosis review supports desiccation tolerance as reversible
+    survival of near-complete water loss.
+- reference: DOI:10.3390/genes14091803
+  snippet: Deinococcus radiodurans, a Gram-positive extremophilic bacterium, is a
+    remarkable example of such an organism, showcasing an impressive resistance to a
+    wide array of stressors, including ionizing radiation, desiccation, UV radiation,
+    and oxidizing agents
+  notes: 'Organism example: Deinococcus radiodurans is desiccation-tolerant, sharing
+    DNA-repair machinery with its radiation tolerance.'
+curation_history:
+- timestamp: '2026-05-28T00:00:00Z'
+  curator: claude
+  action: PROPOSED_FROM_RESEARCH
+  changes: Proposed candidate ENVIRONMENT trait (desiccation tolerance / anhydrobiosis)
+    from literature research to fill the water-availability coverage gap.
+  llm_assisted: true

data/traits/environment/ionizing_radiation_tolerant.yaml

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+identifier: traitmech:000008
+label: ionizing radiation tolerant
+definition: An environmental tolerance in which an organism survives high doses of
+  ionizing radiation (e.g. gamma rays), typically via efficient repair of DNA
+  double-strand breaks and protection of the proteome from oxidative damage.
+definition_source: DOI:10.3390/genes14091803
+trait_category: ENVIRONMENT
+term_kind: CLASS
+mapping_status: PROPOSED
+parent_traits:
+- traitmech:000007
+synonyms:
+- synonym_text: gamma radiation resistant
+  synonym_type: NARROW_SYNONYM
+  source: DOI:10.3390/genes14091803
+evidence:
+- reference: DOI:10.3390/genes14091803
+  snippet: Deinococcus radiodurans R1 demonstrates a significantly higher radiation
+    resistance with D10 values exceeding 12 kGy for gamma radiation and 700 J/m2 for
+    UV-C radiation
+  notes: 'Organism example: Deinococcus radiodurans tolerates gamma (ionizing)
+    radiation D10 doses exceeding 12 kGy.'
+- reference: DOI:10.1101/cshperspect.a012765
+  snippet: A strong correlation has been shown between intracellular Mn/Fe concentration
+    ratios and bacterial resistance to radiation
+  notes: Mechanism support — manganese-mediated oxidative-damage protection underlies
+    survival of lethal ionizing-radiation doses.
+curation_history:
+- timestamp: '2026-05-28T00:00:00Z'
+  curator: claude
+  action: PROPOSED_FROM_RESEARCH
+  changes: Proposed candidate ENVIRONMENT trait (ionizing/gamma radiation tolerance)
+    from literature research; sub-variant of radiotolerant.
+  llm_assisted: true

data/traits/environment/mercury_tolerant.yaml

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+identifier: traitmech:000016
+label: mercury tolerant
+definition: A metal tolerance in which an organism grows in the presence of toxic
+  inorganic or organic mercury compounds, typically via the mer operon, whose
+  mercuric reductase (MerA) reduces reactive Hg(II) to volatile Hg(0).
+definition_source: DOI:10.1016/S0168-6445(03)00046-9
+trait_category: ENVIRONMENT
+term_kind: CLASS
+mapping_status: PROPOSED
+parent_traits:
+- traitmech:000012
+synonyms:
+- synonym_text: mercury resistant
+  synonym_type: RELATED_SYNONYM
+  source: DOI:10.1016/S0168-6445(03)00046-9
+evidence:
+- reference: DOI:10.1016/S0168-6445(03)00046-9
+  snippet: Bacterial resistance to inorganic and organic mercury compounds (HgR) is
+    one of the most widely observed phenotypes in eubacteria
+  notes: Review supports mercury resistance as a widespread bacterial phenotype
+    mediated by MerA, "that reduces reactive ionic Hg(II) to volatile, relatively
+    inert, monoatomic Hg(0) vapor".
+- reference: PMID:12829273
+  snippet: CBA efflux pumps driven by proteins of the resistance-nodulation-cell
+    division superfamily, P-type ATPases, cation diffusion facilitator and chromate
+    proteins
+  notes: Heavy-metal resistance review situates mercury detoxification within the
+    broader prokaryotic metal-resistance machinery.
+curation_history:
+- timestamp: '2026-05-28T00:00:00Z'
+  curator: claude
+  action: PROPOSED_FROM_RESEARCH
+  changes: Proposed candidate ENVIRONMENT trait (mercury tolerance) from literature
+    research; metal-specific sub-variant of metal tolerant.
+  llm_assisted: true

data/traits/environment/metal_tolerant.yaml

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+identifier: traitmech:000012
+label: metal tolerant
+definition: An environmental tolerance in which an organism grows in the presence of
+  elevated concentrations of toxic heavy-metal or metalloid ions, typically via
+  efflux-based resistance determinants (RND-family CBA pumps, P-type ATPases, and
+  cation diffusion facilitators).
+definition_source: PMID:12829273
+trait_category: ENVIRONMENT
+term_kind: CLASS
+mapping_status: PROPOSED
+parent_traits:
+- METPO:1000059
+synonyms:
+- synonym_text: metallophilic
+  synonym_type: RELATED_SYNONYM
+  source: DOI:10.3389/fmicb.2020.00047
+- synonym_text: heavy metal resistant
+  synonym_type: RELATED_SYNONYM
+  source: PMID:12829273
+evidence:
+- reference: PMID:12829273
+  snippet: CBA efflux pumps driven by proteins of the resistance-nodulation-cell
+    division superfamily, P-type ATPases, cation diffusion facilitator and chromate
+    proteins
+  notes: Review of efflux-mediated heavy-metal resistance supports active metal
+    export as the dominant prokaryotic tolerance mechanism.
+- reference: DOI:10.3389/fmicb.2020.00047
+  snippet: This metallophilic strain BS1, harbors numerous gene clusters encoding
+    metal-resistance determinants enabling detoxification of transition metal ions
+    and complexes
+  notes: 'Organism example: Cupriavidus metallidurans is the model metallophilic
+    bacterium tolerating many toxic metals via dedicated resistance gene clusters.'
+curation_history:
+- timestamp: '2026-05-28T00:00:00Z'
+  curator: claude
+  action: PROPOSED_FROM_RESEARCH
+  changes: Proposed candidate ENVIRONMENT trait (general heavy-metal/metalloid
+    tolerance) from literature research to fill the metal-tolerance coverage gap.
+    Parent of the metal-specific sub-variants.
+  llm_assisted: true

data/traits/environment/obligately_piezophilic.yaml

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+identifier: traitmech:000002
+label: obligately piezophilic
+definition: A pressure growth preference in which an organism requires elevated
+  hydrostatic pressure for growth and is unable to grow at atmospheric pressure
+  (0.1 MPa).
+definition_source: DOI:10.1038/srep27289
+trait_category: ENVIRONMENT
+term_kind: CLASS
+mapping_status: PROPOSED
+parent_traits:
+- traitmech:000001
+synonyms:
+- synonym_text: obligate piezophile
+  synonym_type: EXACT_SYNONYM
+  source: DOI:10.1038/srep27289
+evidence:
+- reference: DOI:10.1038/srep27289
+  snippet: High hydrostatic pressure adaptive strategies in an obligate piezophile
+    Pyrococcus yayanosii
+  notes: 'Organism example: Pyrococcus yayanosii is an obligate piezophile that
+    requires high hydrostatic pressure for growth.'
+- reference: DOI:10.1099/ijsem.0.001671
+  snippet: growth range of 80-140 MPa (optimum, 120 MPa) at 6 degrees C
+  notes: 'Organism example: Colwellia marinimaniae MTCD1 grows only at high pressure
+    (80-140 MPa) and does not grow near atmospheric pressure.'
+curation_history:
+- timestamp: '2026-05-28T00:00:00Z'
+  curator: claude
+  action: PROPOSED_FROM_RESEARCH
+  changes: Proposed candidate ENVIRONMENT trait (obligate high-pressure requirement)
+    from literature research; sub-variant of piezophilic. Backed by two obligate-
+    piezophile organism examples.
+  llm_assisted: true

data/traits/environment/piezophilic.yaml

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+identifier: traitmech:000001
+label: piezophilic
+definition: An environmental growth preference in which an organism grows optimally
+  at hydrostatic pressures substantially above atmospheric pressure (0.1 MPa),
+  characteristic of deep-sea and deep-subsurface microorganisms.
+definition_source: DOI:10.3389/fmolb.2022.1058381
+trait_category: ENVIRONMENT
+term_kind: CLASS
+mapping_status: PROPOSED
+parent_traits:
+- METPO:1000059
+synonyms:
+- synonym_text: barophilic
+  synonym_type: RELATED_SYNONYM
+  source: DOI:10.3389/fmolb.2022.1058381
+- synonym_text: piezophile
+  synonym_type: EXACT_SYNONYM
+  source: DOI:10.3389/fmolb.2022.1058381
+evidence:
+- reference: DOI:10.3389/fmolb.2022.1058381
+  snippet: Microorganisms adapted to HHP are usually known as piezophiles, referring
+    to their preference for high pressure
+  notes: Membrane-lipid adaptation review supports the definition of piezophiles as
+    high-hydrostatic-pressure-adapted organisms, with adaptation involving unsaturated
+    and branched-chain fatty acids.
+- reference: DOI:10.1099/ijsem.0.001671
+  snippet: growth range of 80-140 MPa (optimum, 120 MPa) at 6 degrees C
+  notes: 'Organism example: Colwellia marinimaniae strain MTCD1, the most piezophilic
+    organism described, grows optimally at 120 MPa.'
+curation_history:
+- timestamp: '2026-05-28T00:00:00Z'
+  curator: claude
+  action: PROPOSED_FROM_RESEARCH
+  changes: Proposed candidate ENVIRONMENT trait (high-hydrostatic-pressure growth
+    preference) from literature research to fill the pressure-tolerance coverage gap.
+    Backed by a piezophile adaptation review and a deep-sea organism example.
+  llm_assisted: true

data/traits/environment/piezotolerant.yaml

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+identifier: traitmech:000003
+label: piezotolerant
+definition: A pressure growth preference in which an organism can grow under elevated
+  hydrostatic pressure but grows at similar or faster rates at atmospheric pressure
+  (0.1 MPa).
+definition_source: DOI:10.3389/fmolb.2022.1058381
+trait_category: ENVIRONMENT
+term_kind: CLASS
+mapping_status: PROPOSED
+parent_traits:
+- METPO:1000059
+synonyms:
+- synonym_text: barotolerant
+  synonym_type: RELATED_SYNONYM
+  source: DOI:10.3389/fmolb.2022.1058381
+evidence:
+- reference: DOI:10.3389/fmolb.2022.1058381
+  snippet: Microorganisms adapted to HHP are usually known as piezophiles, referring
+    to their preference for high pressure
+  notes: Pressure-adaptation review distinguishes piezotolerant organisms, which
+    withstand high hydrostatic pressure but grow at similar or faster rates at
+    atmospheric pressure, from obligate piezophiles.
+- reference: DOI:10.1099/ijsem.0.001671
+  snippet: growth range of 80-140 MPa (optimum, 120 MPa) at 6 degrees C
+  notes: Provides the contrasting obligate-piezophile reference point against which
+    piezotolerant (atmospheric-capable) growth is defined.
+curation_history:
+- timestamp: '2026-05-28T00:00:00Z'
+  curator: claude
+  action: PROPOSED_FROM_RESEARCH
+  changes: Proposed candidate ENVIRONMENT trait (pressure-tolerant growth) from
+    literature research to complete the pressure-preference axis alongside
+    piezophilic and obligately piezophilic.
+  llm_assisted: true